Table 2.

Percentage of simulation runs indicating matches between planted and identified motifs pertaining to case-control data set 2, and the significance levels of the identified motifs

RR
2.0
1.5
1.2
Number of matchesa
Number of matches
Number of matches
Planted Motif length
μ1
No. of polymorphic sites
0
1
2
3
4
5
6
p-value
0
1
2
3
4
5
6
p-value
0
1
2
3
4
5
6
p-value
100 0 0 0 0 100 — — <10-7 0 0 0 55.2 44.8 — — 0.007 43.5 33.9 12.2 10.4 0 — — 0.522
0.2 200 0 0 0 0 100 — — <10-7 0 0 0 57.4 42.6 — — 0.008 46.8 31.5 12.7 9.0 0 — — 0.481
300 0 0 0 0 100 — — <10-7 0 0 0 60.3 39.7 — — 0.011 49.2 35.8 10.1 4.9 0 — — 0.497
4
100 0 0 0 0 100 — — <10-7 0 0 0 56.1 43.9 — — 0.011 25.3 31.6 28.1 14.8 0.2 — — 0.927
0.4 200 0 0 0 0 100 — — <10-7 0 0 0 56.8 43.2 — — 0.011 28.1 32.2 25.7 13.9 0.1 — — 0.931
300 0 0 0 0 100 — — <10-7 0 0 0 59.1 40.9 — — 0.013 28.8 33.6 24.1 13.4 0.1 — — 0.919
100 0 0 0 0 0 0 100 <10-7 0 8.2 13.1 23.7 35.3 18.9 0.8 0.010 19.8 37.2 21.9 18.7 2.4 0 0 0.498
0.2 200 0 0 0 0 0 0 100 <10-7 0 9.5 16.8 22.6 32.2 18.6 0.3 0.011 22.7 34.0 20.8 18.2 4.1 0 0 0.489
300 0 0 0 0 0 0 100 <10-7 0 11.2 12.1 23.9 31.9 20.6 0.3 0.013 22.8 35.3 21.6 18.6 1.7 0 0 0.490
6
100 0 0 0 0 13.3 56.8 29.9 <10-7 0 3.2 8.1 18.6 51.2 18.5 0.4 0.017 35.2 28.3 27.6 8.3 0.6 0 0 0.917
0.4 200 0 0 0 0 14.9 60.3 24.8 <10-7 0 3.2 8.4 16.3 52.7 18.9 0.5 0.018 36.5 25.9 28.5 8.6 0.5 0 0 0.901
300
0
0
0
0
14.7
61.1
24.2
<10-7
0
3.7
8.9
16.1
53.0
17.9
0.4
0.021
37.8
22.7
31.9
7.3
0.3
0
0
0.886

a Number of matches indicate the number of sites and the nucleotides at the sites that match between the motif identified by the algorithm and the planted motif